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Calcium in PDB 7wgr: Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex

Enzymatic activity of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex

All present enzymatic activity of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex:
1.2.4.2;

Other elements in 7wgr:

The structure of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex (pdb code 7wgr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex, PDB code: 7wgr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7wgr

Go back to Calcium Binding Sites List in 7wgr
Calcium binding site 1 out of 2 in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1101

b:43.2
occ:1.00
O A:HIS143 2.6 42.0 1.0
O A:ASP158 2.9 53.4 1.0
OD1 A:ASP156 3.2 45.5 1.0
O A:SER160 3.4 59.2 1.0
OD2 A:ASP156 3.5 45.5 1.0
C A:HIS143 3.6 42.0 1.0
CG A:ASP156 3.7 45.5 1.0
C A:ASP158 3.9 53.4 1.0
C A:SER159 4.4 55.1 1.0
CA A:HIS143 4.4 42.0 1.0
C A:SER160 4.5 59.2 1.0
CA A:SER159 4.5 55.1 1.0
CB A:HIS143 4.5 42.0 1.0
N A:VAL144 4.5 42.4 1.0
N A:SER160 4.6 59.2 1.0
OD2 A:ASP154 4.6 48.3 1.0
N A:SER159 4.6 55.1 1.0
O A:SER159 4.6 55.1 1.0
CA A:VAL144 4.6 42.4 1.0
OD1 A:ASP154 4.7 48.3 1.0
CA A:ASP158 4.9 53.4 1.0
CB A:ASP158 4.9 53.4 1.0
CG A:ASP154 4.9 48.3 1.0

Calcium binding site 2 out of 2 in 7wgr

Go back to Calcium Binding Sites List in 7wgr
Calcium binding site 2 out of 2 in the Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Electron Microscopic Structure of the 2-Oxoglutarate Dehydrogenase (E1) Component of the Human Alpha-Ketoglutarate (2- Oxoglutarate) Dehydrogenase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1101

b:48.3
occ:1.00
OD2 B:ASP156 2.5 46.3 1.0
O B:ASP158 2.5 55.0 1.0
O B:HIS143 2.7 42.0 1.0
CG B:ASP156 3.3 46.3 1.0
OD1 B:ASP156 3.3 46.3 1.0
O B:SER160 3.4 60.9 1.0
C B:HIS143 3.7 42.0 1.0
C B:ASP158 3.7 55.0 1.0
C B:SER159 4.2 56.9 1.0
CA B:SER159 4.2 56.9 1.0
N B:SER159 4.4 56.9 1.0
C B:SER160 4.4 60.9 1.0
CA B:HIS143 4.5 42.0 1.0
N B:SER160 4.5 60.9 1.0
CB B:HIS143 4.5 42.0 1.0
OD1 B:ASP154 4.6 49.2 1.0
N B:VAL144 4.6 43.3 1.0
O B:SER159 4.6 56.9 1.0
CA B:VAL144 4.7 43.3 1.0
CB B:ASP156 4.7 46.3 1.0
OD2 B:ASP154 4.7 49.2 1.0
CA B:ASP158 4.8 55.0 1.0
CB B:ASP158 4.9 55.0 1.0
CG B:ASP154 4.9 49.2 1.0

Reference:

Y.Zhong, Y.Gao, D.Zhou, X.Ma, H.Chen, Y.Xu, W.Yang, X.Yu. Structural Basis For the Activity and Regulation of Human Alpha-Ketoglutarate Dehydrogenase Revealed By Cryo-Em Biochem.Biophys.Res.Commun. V. 602 120 2022.
ISSN: ESSN 1090-2104
DOI: 10.1016/J.BBRC.2022.02.093
Page generated: Fri Jul 19 05:41:51 2024

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